Variant report

Variant	rs2855563
Chromosome Location	chr1:227082346-227082347
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227076139..227079788-chr1:227081535..227086284,4	K562	blood:
2	chr1:227082066..227083584-chr1:227219659..227222645,2	K562	blood:

Variant related genes	Relation type
ENSG00000143801	Chromatin interaction
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10753428	0.81[EUR][1000 genomes]
rs10799368	0.87[EUR][1000 genomes]
rs10916039	0.91[JPT][hapmap]
rs10916054	0.90[EUR][1000 genomes]
rs11405	0.92[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs1150895	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1150896	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11590925	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12039247	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12126209	0.88[EUR][1000 genomes]
rs12128150	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12130758	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12131495	0.88[EUR][1000 genomes]
rs12133772	0.88[EUR][1000 genomes]
rs12133818	0.87[EUR][1000 genomes]
rs12563993	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12749910	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1295621	0.81[EUR][1000 genomes]
rs1295642	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1295644	0.81[EUR][1000 genomes]
rs1295645	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1295648	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1295651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1297990	0.92[CEU][hapmap]
rs1782530	0.81[EUR][1000 genomes]
rs1800678	0.92[CEU][hapmap]
rs2073488	0.81[EUR][1000 genomes]
rs2105822	0.81[EUR][1000 genomes]
rs2236910	0.81[EUR][1000 genomes]
rs2236913	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs2793462	0.81[EUR][1000 genomes]
rs2802267	0.92[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs34741989	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61837761	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61837762	0.88[EUR][1000 genomes]
rs61837763	0.88[EUR][1000 genomes]
rs6426542	0.84[EUR][1000 genomes]
rs6426543	0.87[EUR][1000 genomes]
rs6426545	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6426546	0.87[EUR][1000 genomes]
rs6660109	0.88[EUR][1000 genomes]
rs6660716	0.87[EUR][1000 genomes]
rs6663555	0.88[EUR][1000 genomes]
rs6678134	0.87[EUR][1000 genomes]
rs743601	0.81[EUR][1000 genomes]
rs743602	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7525811	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7553957	0.88[EUR][1000 genomes]
rs835661	1.00[LWK][hapmap]
rs9660802	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2855563	LEFTY1	cis	cerebellum	SCAN
rs2855563	PYCR2	cis	parietal	SCAN
rs2855563	GJC2	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227059800-227095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:227069400-227085000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:227069400-227087800	Weak transcription	HMEC	breast
4	chr1:227069400-227102800	Weak transcription	K562	blood
5	chr1:227070800-227088200	Weak transcription	Fetal Brain Male	brain
6	chr1:227071000-227089000	Strong transcription	Stomach Smooth Muscle	stomach
7	chr1:227071200-227086800	Weak transcription	NHDF-Ad	bronchial
8	chr1:227071200-227088400	Weak transcription	Hela-S3	cervix
9	chr1:227071200-227091400	Weak transcription	Osteobl	bone
10	chr1:227071400-227084400	Strong transcription	Fetal Intestine Small	intestine
11	chr1:227071600-227087000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:227071800-227102400	Weak transcription	Small Intestine	intestine
13	chr1:227072200-227087000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:227072200-227091800	Weak transcription	Fetal Kidney	kidney
15	chr1:227072200-227100400	Weak transcription	Stomach Mucosa	stomach
16	chr1:227072800-227083600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:227073000-227085200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:227073400-227084400	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:227073400-227084600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:227073400-227088600	Strong transcription	Fetal Stomach	stomach
21	chr1:227073400-227092200	Strong transcription	Pancreas	Pancrea
22	chr1:227073800-227100600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:227074200-227083000	Strong transcription	Colon Smooth Muscle	Colon
24	chr1:227074200-227091800	Weak transcription	Fetal Heart	heart
25	chr1:227074800-227090000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:227074800-227090200	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:227075000-227084200	Strong transcription	Gastric	stomach
28	chr1:227075000-227085400	Strong transcription	Ovary	ovary
29	chr1:227075000-227087400	Weak transcription	Primary B cells from cord blood	blood
30	chr1:227075000-227088800	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:227075200-227083200	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr1:227075200-227087000	Weak transcription	GM12878-XiMat	blood
33	chr1:227075200-227091800	Weak transcription	Right Atrium	heart
34	chr1:227075400-227085000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr1:227075400-227088800	Strong transcription	Liver	Liver
36	chr1:227075600-227083200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:227075600-227083800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:227075600-227088200	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr1:227075800-227084600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr1:227076400-227082600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:227076400-227083400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:227076400-227084000	Strong transcription	Aorta	Aorta
43	chr1:227076600-227087400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:227077800-227085400	Strong transcription	Rectal Smooth Muscle	rectum
45	chr1:227078000-227082400	Strong transcription	NHLF	lung
46	chr1:227078000-227084800	Strong transcription	Brain Cingulate Gyrus	brain
47	chr1:227078200-227083600	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:227078600-227091600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr1:227079000-227087200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:227079400-227084600	Strong transcription	Brain Hippocampus Middle	brain

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